Sequence input.

MSKVPRNFRL LEELEKGEKG FGPESCSYGL ADSDDITMTK WNGTILGPPH SNHENRIYSL
SIDCGPNYPD SPPKVTFISK INLPCVNPTT GEVQTDFHTL RDWKRAYTME TLLLDLRKEM
ATPANKKLRQ PKEGETF

The first step is to introduce the sequence into the "SWISS-MODEL First Approach mode" web server and to launch the process [See Figure].

Recepction of a confirmatory mail.

Recepction of a mail containing different processes followed by SWISS-MODEL.

1. SWISS-MODEL perform a homology searching on a 3D structure database using BLASTP2 and the database "ExNRL-3D". The results are sorted according to the BLAST P(N) score:

     AlignMaster output
     ============================================================
     
     Length of target sequence: 137 residues
     
     Searching sequences of known 3D structures
     Found 12UCE.pdb with P(N)=5.0e-12
     Found 11AYZ.pdb with P(N)=1.2e-08
     Found 11AAK.pdb with P(N)=5.3e-08
     Found 12AAK.pdb with P(N)=5.3e-08
     Found 11UCZ.pdb with P(N)=1.1e-07
     Found 12UCZ.pdb with P(N)=1.1e-07
     Found 11A3S.pdb with P(N)=1.0e-05

2. The  "SIM" program selects all the templates with a sequence identity higher that 25% and an aligned region over 20 residues:

     Extracting template sequences
     
     Running pair-wise alignments with target sequence
     Sequence identity of templates with target:
     
     12UCE.pdb: 22.85 % identity
     11AYZ.pdb: 27.8 % identity
     11AAK.pdb: 17.15 % identity
     12AAK.pdb: 17.15 % identity
     11UCZ.pdb: 29.6 % identity
     12UCZ.pdb: 29.6 % identity
     11A3S.pdb: 22.5 % identity
     
     Looking for template groups
     Global alignment overview:
     
     Taget Sequence: |====================================================================|
     12UCE.pdb       |                  -------------------------------------------------
     11AYZ.pdb       |                    ------------------------------------------------
     11AAK.pdb       |               -----------------------------------------------------
     12AAK.pdb       |               -----------------------------------------------------
     11UCZ.pdb       |                 --------------------------                        
     12UCZ.pdb       |                 --------------------------                        
     11A3S.pdb       |                 --------------------------------------------------
     
     AlignMaster found 1 regions to model separately:
             1: Using template(s)   11A3S.pdb 11AAK.pdb 11AYZ.pdb 11UCZ.pdb 12AAK.pdb 12UCE.pdb 12UCZ.pdb
     
     12UCE.pdb has been rejected,  too low similarity with Target sequence (22.85 % identity.)
     11AAK.pdb has been rejected,  too low similarity with Target sequence (17.15 % identity.)
     12AAK.pdb has been rejected,  too low similarity with Target sequence (17.15 % identity.)
     11A3S.pdb has been rejected,  too low similarity with Target sequence (22.5 % identity.)

3. In this step the "ProModII" program input file is generated. This program, using the templates from the "ExPDB" database, generates all the models from the input sequence:

     Creating Batch files for ProMod (if any):
             Batch.1: residues 30 - 137 of submitted sequence.
     
     Exiting AlignMaster
     
     
     ProModII trace log for Batch.1
     ============================================================
     
     ProModII: Loading Template: 11AYZ.pdb
     ProModII: Loading Template: 11UCZ.pdb
     ProModII: Loading Template: 12UCZ.pdb
     ProModII: Loading Raw Sequence
     ProModII: Iterative Template Fitting
     ProModII: Iterative Template Fitting
     ProModII: Generating Structural Alignment
     ProModII: Aligning Raw Sequence
     ProModII: Refining Raw Sequence Alignment
     ProModII: Weighting Backbones
     ProModII: Averaging Sidechains
     ProModII: Adding Missing Sidechains
     ProModII: Small Ligation (C-N < 3.0A) ignored;
     ProModII: GROMOS will repair it at residue ASP 73
     ProModII: Building CSP loop with anchor residues THR 60 and GLU 63
     ProModII:   Number of Ligations found:  (1)
     ProModII: all loops are bad; continuing CSP with larger segment
     ProModII: Building CSP loop with anchor residues PRO 59 and GLU 63
     ProModII:   Number of Ligations found:  (10)
     ProModII: ACCEPTING loop    5: clash=   1 FF=         53.8 PP=-18.41
     ProModII: Dumping Preliminary Model
     ProModII: Dumping Sequence Alignment
     ProModII: Done.

4. In the last step, the "Gromos96" program optimizes the model(s) using a energy minimization process:

     Gromos96 trace log for Batch.1
     ============================================================
     
     Now running PROCS1 on file batch-procs0.dat ... Done.
     Now running PROCS2 on file batch-procs1.dat ... Done.
     Now running PROGMT on file batch-procs2.dat ... Done.
     Now running PROGCH on file batch-procs2.dat ... Done.
     Now running PROMD on file batch-progch.dat ... Done.
     Now running PROMD on file batch-promd0.dat ... Done.
     Detection of SS-Bonds within batch ...

Recepction of a mail with the 3D coordinates of the model.